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Browsing by Author "Mueller, Lukas A."

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    Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell
    Villarino, Gonzalo H.; Hu, Qiwen; Scanlon, Michael J.; Mueller, Lukas A.; Bombarely, Aureliano; Mattson, Neil S. (MDPI, 2017-08-03)
    One of the primary objectives of plant biotechnology is to increase resistance to abiotic stresses, such as salinity. Salinity is a major abiotic stress and increasing crop resistant to salt continues to the present day as a major challenge. Salt stress disturbs cellular environment leading to protein misfolding, affecting normal plant growth and causing agricultural losses worldwide. The advent of state-of-the-art technologies such as high throughput mRNA sequencing (RNA-seq) has revolutionized whole-transcriptome analysis by allowing, with high precision, to measure changes in gene expression. In this work, we used tissue-specific RNA-seq to gain insight into the Petunia hybrida transcriptional responses under NaCl stress using a controlled hydroponic system. Roots and leaves samples were taken from a continuum of 48 h of acute 150 mM NaCl. This analysis revealed a set of tissue and time point specific differentially expressed genes, such as genes related to transport, signal transduction, ion homeostasis as well as novel and undescribed genes, such as Peaxi162Scf00003g04130 and Peaxi162Scf00589g00323 expressed only in roots under salt stress. In this work, we identified early and late expressed genes in response to salt stress while providing a core of differentially express genes across all time points and tissues, including the trehalose-6-phosphate synthase 1 (TPS1), a glycosyltransferase reported in salt tolerance in other species. To test the function of the novel petunia TPS1 allele, we cloned and showed that TPS1 is a functional plant gene capable of complementing the trehalose biosynthesis pathway in a yeast tps1 mutant. The list of candidate genes to enhance salt tolerance provided in this work constitutes a major effort to better understand the detrimental effects of salinity in petunia with direct implications for other economically important Solanaceous species.
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    Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica
    Carlson, Keisha D.; Fernandez-Pozo, Noe; Bombarely, Aureliano; Pisupati, Rahul; Mueller, Lukas A.; Madlung, Andreas (2017-08-23)
    Background Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation. Arabidopsis suecica is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of A. suecica grown in a common garden. Results To determine the degree of genomic similarity between different populations of A. suecica, we obtained transcriptomic sequence, quantified SNP variation within the gene space, and analyzed gene expression levels genome-wide from leaf material grown in controlled lab conditions. Despite their origin from the same progenitor species, the two accessions of A. suecica used in our study show genomic and transcriptomic variation. We report significant gene expression differences between the accessions, mostly in genes with stress-related functions. Among the differentially expressed genes, there are a surprising number of homoeologs coordinately regulated between sister accessions. Conclusions Many of these homoeologous genes and other differentially expressed genes affect transpiration and stomatal regulation, suggesting that they might be involved in the establishment of the phenotypic differences between the two accessions.
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    A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency
    Edwards, Kieron D.; Fernandez-Pozo, Noe; Drake-Stowe, Katherine; Humphry, Matthew Edward; Evans, Andy D.; Bombarely, Aureliano; Allen, Fraser; Hurst, R.; White, B.; Kernodle, Sheri P.; Bromley, Jennifer R.; Sanchez-Tamburrino, Juan Pablo; Lewis, Ramsey S.; Mueller, Lukas A. (2017-06-19)
    Background Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging because it is an allotetraploid, likely arising from hybridisation between diploid N. sylvestris and N. tomentosiformis ancestors. A draft assembly was recently published for N. tabacum, but because of the aforementioned genome complexities it was of limited utility due to a high level of fragmentation. Results Here we report an improved tobacco genome assembly, which, aided by the application of optical mapping, achieves an N50 size of 2.17 Mb and enables anchoring of 64% of the genome to pseudomolecules; a significant increase from the previous value of 19%. We use this assembly to identify two homeologous genes that explain the differentiation of the burley tobacco market class, with potential for greater understanding of Nitrogen Utilization Efficiency and Nitrogen Use Efficiency in plants; an important trait for future sustainability of agricultural production. Conclusions Development of an improved genome assembly for N. tabacum enables what we believe to be the first successful map-based gene discovery for the species, and demonstrates the value of an improved assembly for future research in this model and commercially-important species.
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    The Sol Genomics Network (SGN)-from genotype to phenotype to breeding
    Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.; Saha, Surya; Tecle, Isaak Y.; Strickler, Susan R.; Bombarely, Aureliano; Fisher-York, Thomas; Pujar, Anuradha; Foerster, Hartmut; Yan, Aimin; Mueller, Lukas A. (2015-01-28)
    The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, and analysis tools for the Solanaceae family and close relatives. SGN hosts whole genome data for an increasing number of Solanaceae family members including tomato, potato, pepper, eggplant, tobacco and Nicotiana benthamiana. The database also stores loci and phenotype data, which researchers can upload and edit with user-friendly web interfaces. Tools such as BLAST, GBrowse and JBrowse for browsing genomes, expression and map data viewers, a locus community annotation system and a QTL analysis tools are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called the SGN VIGS tool. With the growing genomic and phenotypic data in the database, SGN is now advancing to develop new web-based breeding tools and implement the code and database structure for other species or clade-specific databases.
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    The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality
    Bally, Ian S. E.; Bombarely, Aureliano; Chambers, Alan H.; Cohen, Yuval; Dillon, Natalie L.; Innes, David J.; Islas-Osuna, María A.; Kuhn, David N.; Mueller, Lukas A.; Ophir, Ron; Rambani, Aditi; Sherman, Amir; Yan, Haidong (2021-02-22)
    Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.